Software
- BioGrep - Python library that is a (very partial) port of Bio::Grep from perl. Allows you to make simple searches in databases using exact match programs. Currently only supports vmatch. Undocumented and sparse. Help me if you like! BioGrep-0.4.tar.gz
- pwfile - Program to manage an encrypted file containing your passwords from the commandline. An experiment in "run-of-the-mill-mediocre" coding, so dealing with the code is not advisable. Still in development. pwfile-0.2.tar.gz
- libgenc - A little bit of a work in progress, but getting usable. A library with generic C data structures. sourceforge site
- bioports - MacPorts is an outsdanding project to port a lot of GNU/Linux and other well-known UNIX utilities that aren't included with Mac OS X by default. Since Computational Biology isn't that popular, and becoming a developer on MacPorts requires some amount of attention, I maintain my own set of ports here. To use it, simply add a line of
file:///path/to/bioports to your /opt/local/etc/macports/sources.conf file. bioports-8.tar.gz
- iParameterEstimation - Should you want to estimate parameters for a hidden Markov Model, especially for gene finding, this iPE is your jam. Brent Lab iPE page
